Question: Favorite Splice Site Prediction/Evaluation Tools
9
gravatar for Alex Paciorkowski
6.6 years ago by
Rochester, NY USA
Alex Paciorkowski3.3k wrote:

Does anyone have a favorite splice site prediction / evaluation tool? (This would be for evaluating variants in the human genome). I am familiar with the Human Splicing Finder, but am looking to try others. Open-source would be ideal, and if possible something that can be scripted into a workflow. Thanks.

splicing prediction • 14k views
ADD COMMENTlink modified 5.3 years ago by Malachi Griffith17k • written 6.6 years ago by Alex Paciorkowski3.3k
5
gravatar for Malachi Griffith
6.6 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

A review of some potentially relevant tools, databases, algorithms, etc. can be found in Table 1.2 on page 52-53 of this thesis.

Also this post is highly relevant: Alternative splicing detection

ADD COMMENTlink modified 5.3 years ago • written 6.6 years ago by Malachi Griffith17k

I really appreciate your sharing this -- thank you.

ADD REPLYlink written 6.6 years ago by Alex Paciorkowski3.3k
3
gravatar for swbarnes2
6.6 years ago by
swbarnes25.9k
United States
swbarnes25.9k wrote:

This is the one I've used for a while, but its quite old:

http://www.fruitfly.org/seq_tools/splice.html

Can't say I have any hard evidence of its accuracy, but it's easy to use. But I don't see how to incorporate it into a script

ADD COMMENTlink written 6.6 years ago by swbarnes25.9k

Thanks, I will definitely check this one out.

And I know -- it doesn't apparently bode well for one's research program to be asking about tools to evaluate intronic sequence...

ADD REPLYlink written 6.6 years ago by Alex Paciorkowski3.3k
3
gravatar for Venkatesh
6.0 years ago by
Venkatesh30
Venkatesh30 wrote:

Hi Alex, sorry if this reply is a bit late.

I have used Human Splicing Finder and GeneSplicer but I would recommend AspAlt (Alternative-splicing and Alternative Transcription) tool along with EuSplice.

Unfortunately, these are not open-source but the accuracy is impressive. They follow a scoring system for predicted cryptic splice sites and compare them with known splice junctions which I found useful. Again this is only my opinion, comments welcome!

HTH,

Venkatesh Patel

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Venkatesh30

Hi,

as Alex, I would like to score the impact of the mutations within splice sites and I've found this thread. Apparently it is not that evident to find the right tool to do that, so I write just in case someone has further ideas. Note that I am not interested -at that moment- in finding mutations leading to cryptic splice sites, but to score the importance of mutations in already known splice sites (according to variant effect predictor, for instance)

I already checked MaxEntScan and HumanSpliceFinder, but I do not find how to use them in a script (which I need!)

thanks, david

ADD REPLYlink written 5.8 years ago by david.tamborero0
2
gravatar for jjmerkin
6.6 years ago by
jjmerkin20
jjmerkin20 wrote:

you can use maxent 5'ss or maxent 3'ss to evaluate them. a former post-doc in my lab (before i joined) developed it. the model gives you a splice site strength in units of bits, where higher values correspond to better splice sites. values below 0 tend to be annotation errors or have something weird going on. bits are additive, so you can subtract the variant's score from that of the consensus to determine the expected effect on splicing.

note that maxent does not accurately model u12 (ATAC) introns.

ADD COMMENTlink written 6.6 years ago by jjmerkin20
2
gravatar for Christoph Thieme
6.5 years ago by
Christoph Thieme20 wrote:

I just came over here to ask the same question with a focus on tools for plant RNA splice site prediction... Due to my best knowledge genesplicer (Pertea et al., 2001) is the latest available tool for A. thaliana. Another one is from the Brunak group: NetGene2 (Hebsgaard et al., 1996). I can't believe that there wasn't any progress in this field for the last five to ten years?

ADD COMMENTlink written 6.5 years ago by Christoph Thieme20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1478 users visited in the last hour